The U.S. Army announced it was dropping sexual-assault charges against Brig. Gen. Jeffrey Sinclair in exchange for his plea to less-serious charges of misconduct. The plea bargain would end the trial of the highest-ranking officer ever to face such charges and one of the most closely watched military trials in recent history.The trial may end, but the controversy will continue. While he denied the assault, Sinclair admitted to having a long-standing affair with a soldier under his command, which under military law is considered an abuse of power.Sinclair’s conduct is just one of a series of black eyes for the military and only begins to scratch the surface of the overall problem. A report from the Department of Defense’s Sexual Assault Prevention and Response Office listed 3,374 reported assaults in 2012 a 6 percent increase in reported assaults over the previous year. However, the reported assaults pale in comparison with the estimated unreported assaults. In 2012, the number of sexual assaults left unreported rose to an estimated 26,000.Sinclair’s plea bargain has led advocacy groups to question whether the military is capable of fairly prosecuting such crimes. The plea bargain has also focused attention on a contentious and unusual battle in the U.S. Senate. Two Democrats, both who happen to be female, have pointed to the Sinclair case as the answer for the following question: “Should commanders decide whether prosecutors pursue charges in military court?”The judge, Col. James Pohl, halted Sinclair’s trial, citing information that a commander had improperly influenced prosecutors, using “unlawful command influence” to press the case in order to appear tough on sexual assaults.The claim was the result of a letter Capt. Cassie L. Fowler, the victim’s special counsel, sent to Lt. Gen. Joseph Anderson, commander at Ft. Bragg. The letter asked Anderson to reject a plea offer, “Allowing the accused to characterize this relationship as a consensual affair would only strengthen the arguments of those individuals that believe the prosecution of sexual assault should be taken away from the Army.”The rationale behind unlawful command influence, according to the New York Times, is to prevent senior commanders from trying to influence military justice, ensuring that cases are prosecuted based on legal merit alone. Anderson asked prosecutors to reject any plea from Sinclair.New York Sen. Kristen Gillibrand proposed legislation to take prosecution decisions out of the chain of command. The bill did not survive a filibuster and was defeated.In a recent op-ed in the New York Daily News, Gillibrand wrote, "We will work harder than ever in the coming year to strengthen our military by taking sexual assaults and other major crimes out of the chain of command — so that no victim is compelled to turn to his or her boss to ask for justice," she wrote. "We need every case to move forward based solely on the evidence and judged solely on the merits, not political pressure or other nonlegal considerations."Missouri Sen. Claire McCaskill disagreed. "As a former sex-crimes prosecutor, Claire knows how difficult these cases can be, and this case is obviously a complicated one," McCaskill spokeswoman Sarah Feldman told The National Journal. "But one of its lessons highlights what we already know — that commanders are often more aggressive than prosecutors in pursuing prosecutions.""If this court-martial (Sinclair’s) had been handled by prosecutors alone, it would not have gone to trial," said McCaskill's office in a press release.Gillibrand’s proposal, although lacking sufficient support, did not go far enough. With unreported sexual assault on the rise in the military, and with men entrenched in leadership positions, lawmakers should consider removing sexual-assault investigations and prosecutions out of the military system and into civilian courts.Matthew T. Mangino is of counsel with Luxenberg, Garbett, Kelly & George P.C. His book “The Executioner’s Toll, 2010” is due out this summer. You can reach him at www.mattmangino.com and follow him on Twitter at @MatthewTMangino.